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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ), 'gf_id' => 'HOM05D001334', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001334' ), 'data_identifier' => 'HOM05D001334', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001334', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27700' => 'bna', 'A03p32330' => 'bna', 'A04p02910' => 'bna', 'A04p32140' => 'bna', 'A05p02840' => 'bna', 'A05p16580' => 'bna', 'A09p20210' => 'bna', 'A10p29450' => 'bna', 'Aa31LG1G23930' => 'aar', 'Aa31LG1G23970' => 'aar', 'Aa31LG5G10940' => 'aar', 'Aa31LG9G13300' => 'aar', 'Aa31sc24G160' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3414' => 'aag', 'Actinidia05907' => 'ach', 'Actinidia08081' => 'ach', 'Actinidia09368' => 'ach', 'Actinidia20292' => 'ach', 'Actinidia30666' => 'ach', 'Actinidia36183' => 'ach', 'Ah.02g130680' => 'amhyb', 'Ah.04g152010' => 'amhyb', 'Ah.10g032590' => 'amhyb', 'AL1G52930' => 'aly', 'AL3G10320' => 'aly', 'AL4G40680' => 'aly', 'AL5G39440' => 'aly', 'AL6G17080' => 'aly', 'AL8G17292' => 'aly', 'AL8G17294' => 'aly', 'Aqoxy1G00275' => 'aox', 'Aqoxy3G01484' => 'aox', 'Aqoxy5G03448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2P743F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.986X03' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9EZ8VA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BRH2YL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BY24CF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C24CLM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MJ7V8R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PNPF4F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UE98G4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZHD4SG' => 'arhy', 'AT2G42320' => 'ath', 'AT3G01810' => 'ath', 'AT3G57780' => 'ath', 'AT5G06930' => 'ath', 'AT5G43230' => 'ath', 'ATR0605G057' => 'atr', 'ATR0686G145' => 'atr', 'ATR0686G210' => 'atr', 'Atru.chr1.959' => 'acertr', 'Atru.chr1.960' => 'acertr', 'Atru.chr1.988' => 'acertr', 'Atru.chr11.2287' => 'acertr', 'Atru.chr6.2524' => 'acertr', 'AUR62005587' => 'cqu', 'AUR62018233' => 'cqu', 'AUR62024143' => 'cqu', 'AUR62024380' => 'cqu', 'AUR62025975' => 'cqu', 'AUR62037769' => 'cqu', 'BcaB02g08294' => 'bca', 'BcaB05g23896' => 'bca', 'BcaB06g29237' => 'bca', 'BcaB07g30591' => 'bca', 'BcaB07g31022' => 'bca', 'BcaC02g07245' => 'bca', 'BcaC02g07249' => 'bca', 'BcaC02g09961' => 'bca', 'BcaC02g12475' => 'bca', 'BcaC04g21942' => 'bca', 'BcaC06g32407' => 'bca', 'BcaC06g32532' => 'bca', 'BcaNung04396' => 'bca', 'BolC3t16207H' => 'bol', 'BolC4t21981H' => 'bol', 'BolC4t25018H' => 'bol', 'BolC4t28462H' => 'bol', 'BolC9t55465H' => 'bol', 'BolC9t59727H' => 'bol', 'BraA02t07809Z' => 'bra', 'BraA03t12403Z' => 'bra', 'BraA04t16014Z' => 'bra', 'BraA04t16015Z' => 'bra', 'BraA04t18668Z' => 'bra', 'BraA05t19276Z' => 'bra', 'BraA09t37632Z' => 'bra', 'BraA10t44989Z' => 'bra', 'C03p39380' => 'bna', 'C04p03450' => 'bna', 'C04p34580' => 'bna', 'C04p69630' => 'bna', 'C07p25780' => 'bna', 'C09p25620' => 'bna', 'C09p69830' => 'bna', 'CAN.G1965.15' => 'can', 'CAN.G370.6' => 'can', 'CAN.G44.14' => 'can', 'CAN.G473.83' => 'can', 'CAN.G554.5' => 'can', 'CAN.G75.6' => 'can', 'CANSAT01G2854' => 'cansat', 'CANSAT64G2685' => 'cansat', 'CARHR075120' => 'chi', 'CARHR137360' => 'chi', 'CARHR168100' => 'chi', 'CARHR180650' => 'chi', 'CARHR180660' => 'chi', 'CARHR182400' => 'chi', 'CARHR206220' => 'chi', 'Carub.0003s0025' => 'cru', 'Carub.0004s2466' => 'cru', 'Carub.0005s2463' => 'cru', 'Carub.0006s0585' => 'cru', 'Carub.0008s0546' => 'cru', 'Ca_04423_v3' => 'car', 'Ca_08489_v3' => 'car', 'Ca_09859_v3' => 'car', 'Ca_18153_v3' => 'car', 'CBR_g40912' => 'cbr', 'Cc06_g16450' => 'ccan', 'Cc07_g00640' => 'ccan', 'Cc11_g16720' => 'ccan', 'CDE02G4462' => 'cde', 'CDE04G0813' => 'cde', 'CDE04G2429' => 'cde', 'CDE09G0866' => 'cde', 'Cfa007248' => 'cfa', 'Cfa009343' => 'cfa', 'Cfa016876' => 'cfa', 'Ciclev10004356m.g' => 'ccl', 'Ciclev10014104m.g' => 'ccl', 'Ciclev10030641m.g' => 'ccl', 'CiPaw.03G053200' => 'cil', 'CiPaw.05G113300' => 'cil', 'CiPaw.06G100300' => 'cil', 'CiPaw.10G029800' => 'cil', 'ClCG04G000530' => 'cla', 'ClCG05G013340' => 'cla', 'COL.COLO4_08741' => 'col', 'COL.COLO4_12824' => 'col', 'COL.COLO4_28719' => 'col', 'Cpa.g.c36879' => 'cpa', 'Cpa.g.c46404' => 'cpa', 'Cpa.g.sc11.25' => 'cpa', 'Cpa.g.sc85.127' => 'cpa', 'Cre10.g446000' => 'cre', 'CsaV3_3G027220' => 'csa', 'CsaV3_4G031530' => 'csa', 'CSS0008134' => 'camsi', 'CSS0030615' => 'camsi', 'CSS0034784' => 'camsi', 'CSS0034870' => 'camsi', 'CSS0040096' => 'camsi', 'DCAR_007010' => 'dca', 'DCAR_013572' => 'dca', 'DCAR_021770' => 'dca', 'DCAR_021773' => 'dca', 'Dinv14812' => 'din', 'Dinv18099' => 'din', 'Dinv24114' => 'din', 'Dinv24115' => 'din', 'Dinv25671' => 'din', 'Dinv33356' => 'din', 'Duzib106G1996' => 'dzi', 'Duzib128G0715' => 'dzi', 'Duzib147G0251' => 'dzi', 'Duzib251G0625' => 'dzi', 'Duzib264G0954' => 'dzi', 'Duzib268G1811' => 'dzi', 'ECA232G2282' => 'eca', 'ECA236G3515' => 'eca', 'ECA246G1985' => 'eca', 'ECA246G4043' => 'eca', 'ECA248G2030' => 'eca', 'EL10Ac2g03216' => 'bvu', 'EL10Ac3g06987' => 'bvu', 'EL10Ac6g13466' => 'bvu', 'Eucgr.A02411' => 'egr', 'Eucgr.H04658' => 'egr', 'Eucgr.I01660' => 'egr', 'Eucgr.J02316' => 'egr', 'Eucgr.J02357' => 'egr', 'FAN02G1478' => 'fan', 'FAN02G1858' => 'fan', 'FAN02G2844' => 'fan', 'FAN05G0787' => 'fan', 'FAN05G0895' => 'fan', 'FAN05G2545' => 'fan', 'FAN05G3330' => 'fan', 'FAN05G3693' => 'fan', 'FAN05G5412' => 'fan', 'FAN07G1880' => 'fan', 'FAN09G0949' => 'fan', 'FAN09G3180' => 'fan', 'FAN09G3832' => 'fan', 'FAN12G2542' => 'fan', 'FAN14G2545' => 'fan', 'FAN14G5932' => 'fan', 'FAN17G1057' => 'fan', 'FAN22G1108' => 'fan', 'FvH4_4g24100' => 'fve', 'FvH4_6g23000' => 'fve', 'FvH4_6g53120' => 'fve', 'Glyma.03G140900' => 'gma', 'Glyma.10G182000' => 'gma', 'Glyma.16G059500' => 'gma', 'Glyma.19G074600' => 'gma', 'Glyma.19G087900' => 'gma', 'Glyma.19G143600' => 'gma', 'Glyma.20G208000' => 'gma', 'Gohir.A01G161100' => 'ghi', 'Gohir.A07G226700' => 'ghi', 'Gohir.A09G124800' => 'ghi', 'Gohir.A10G159800' => 'ghi', 'Gohir.A12G148200' => 'ghi', 'Gohir.D01G148600' => 'ghi', 'Gohir.D07G233900' => 'ghi', 'Gohir.D09G121800' => 'ghi', 'Gohir.D10G084900' => 'ghi', 'Gohir.D11G326901' => 'ghi', 'Gohir.D12G152100' => 'ghi', 'Gorai.001G269300' => 'gra', 'Gorai.002G184400' => 'gra', 'Gorai.006G139400' => 'gra', 'Gorai.007G357600' => 'gra', 'Gorai.008G164500' => 'gra', 'Gorai.011G092300' => 'gra', 'GSVIVG01001814001' => 'vvi', 'GSVIVG01010364001' => 'vvi', 'GSVIVG01033345001' => 'vvi', 'HanXRQChr04g0123381' => 'han', 'HanXRQChr05g0132721' => 'han', 'HanXRQChr09g0256081' => 'han', 'HanXRQChr11g0320581' => 'han', 'HanXRQChr11g0340101' => 'han', 'HanXRQChr15g0474931' => 'han', 'HanXRQChr17g0540311' => 'han', 'Haze_12380' => 'cav', 'Haze_14844' => 'cav', 'Haze_19922' => 'cav', 'Hma1.2p1_0856F.1_g229155' => 'hma', 'Hma1.2p1_1239F.1_g269390' => 'hma', 'HPP92_018944' => 'vpl', 'HPP92_019683' => 'vpl', 'HPP92_024640' => 'vpl', 'Hund06075' => 'sun', 'Hund13055' => 'sun', 'Hund19174' => 'sun', 'Hund24751' => 'sun', 'Lalb_Chr02g0150211' => 'lal', 'Lalb_Chr02g0157811' => 'lal', 'Lalb_Chr20g0110981' => 'lal', 'Lalb_Chr21g0312101' => 'lal', 'Lalb_Chr22g0360491' => 'lal', 'Lalb_Chr25g0287521' => 'lal', 'Lj1g0004478' => 'lja', 'Lj1g0021687' => 'lja', 'Lj2C376G1' => 'lonja', 'Lj3C1065T7' => 'lonja', 'Lj5g0001342' => 'lja', 'Lj7A609T56' => 'lonja', 'Lju124A34T50' => 'lonja', 'Lju41A51T44' => 'lonja', 'Lsat_1_v5_gn_3_135500' => 'lsa', 'Lsat_1_v5_gn_3_29680' => 'lsa', 'Lsat_1_v5_gn_4_185341' => 'lsa', 'Lsat_1_v5_gn_5_163841' => 'lsa', 'Lsat_1_v5_gn_8_79460' => 'lsa', 'Manes.09G030300' => 'mes', 'Manes.12G014000' => 'mes', 'Manes.13G017200' => 'mes', 'Manes.15G158800' => 'mes', 'Manes.17G105300' => 'mes', 'Mapoly0082s0054' => 'mpo', 'MBI01_g05763_MAGBIO' => 'mbi', 'MBI04_g13613_MAGBIO' => 'mbi', 'MBI07_g43637_MAGBIO' => 'mbi', 'MBI08_g17168_MAGBIO' => 'mbi', 'MBI12_g47823_MAGBIO' => 'mbi', 'MBI12_g48107_MAGBIO' => 'mbi', 'MD09G1014400' => 'mdo', 'MD12G1064400' => 'mdo', 'MD13G1115500' => 'mdo', 'MD14G1064600' => 'mdo', 'MD16G1115400' => 'mdo', 'MD17G1014500' => 'mdo', 'Medtr1g075790' => 'mtr', 'Medtr7g092460' => 'mtr', 'MELO3C009076.2' => 'cme', 'MELO3C014866.2' => 'cme', 'Migut.E00030' => 'egut', 'Migut.J01794' => 'egut', 'Migut.K00708' => 'egut', 'Migut.K01449' => 'egut', 'MSTRG.13318' => 'ama', 'MSTRG.15562' => 'ama', 'MSTRG.19886' => 'ama', 'MSTRG.24084' => 'ama', 'MSTRG.6459' => 'ama', 'MSTRG.7989' => 'ama', 'Nitab4.5_0000148g0050' => 'nta', 'Nitab4.5_0000559g0200' => 'nta', 'Nitab4.5_0000581g0030' => 'nta', 'Nitab4.5_0000603g0060' => 'nta', 'Nitab4.5_0001119g0120' => 'nta', 'Nitab4.5_0001439g0020' => 'nta', 'Nitab4.5_0002887g0070' => 'nta', 'Nitab4.5_0002899g0020' => 'nta', 'Nitab4.5_0003477g0010' => 'nta', 'Nitab4.5_0006819g0050' => 'nta', 'Nitab4.5_0007150g0020' => 'nta', 'Nn1g04567' => 'nnu', 'Nn2g15390' => 'nnu', 'Nn3g16523' => 'nnu', 'Nn4g22380' => 'nnu', 'Nn5g28850' => 'nnu', 'Nn6g32386' => 'nnu', 'Nn6g32387' => 'nnu', 'Nn7g36190' => 'nnu', 'Oeu011956.1' => 'oeu', 'Oeu013951.1' => 'oeu', 'Oeu019041.1' => 'oeu', 'Oeu020304.1' => 'oeu', 'Oeu033770.2' => 'oeu', 'Oeu050559.1' => 'oeu', 'Os08g0505200' => 'osa', 'Os09g0487200' => 'osa', 'Os12g0236100' => 'osa', 'Peaxi162Scf00128g01036' => 'pax', 'Peaxi162Scf00128g01045' => 'pax', 'Peaxi162Scf00189g00073' => 'pax', 'Peaxi162Scf00420g00434' => 'pax', 'Peaxi162Scf00700g00136' => 'pax', 'Peaxi162Scf00700g00147' => 'pax', 'Peaxi162Scf00945g00121' => 'pax', 'PGR004G1154' => 'pgr', 'PGR083G1249' => 'pgr', 'PGR119G1858' => 'pgr', 'PGR142G2296' => 'pgr', 'PGSC0003DMG400012931' => 'stu', 'PGSC0003DMG400013428' => 'stu', 'PGSC0003DMG400014918' => 'stu', 'PGSC0003DMG400020262' => 'stu', 'PGSC0003DMG400024981' => 'stu', 'Phvul.001G095700' => 'pvu', 'Phvul.001G137700' => 'pvu', 'Phvul.004G055300' => 'pvu', 'Phvul.008G145301' => 'pvu', 'Potri.001G333200' => 'ptr', 'Potri.006G056800' => 'ptr', 'Potri.008G177500' => 'ptr', 'Potri.010G057700' => 'ptr', 'Potri.016G051500' => 'ptr', 'Pp3c15_3720' => 'ppa', 'Pp3c17_24080' => 'ppa', 'Prupe.1G231700' => 'ppe', 'Prupe.3G303300' => 'ppe', 'Prupe.7G069500' => 'ppe', 'Psat1g084960' => 'psa', 'Psat3g070600' => 'psa', 'Psat3g176160' => 'psa', 'Psat6g117560' => 'psa', 'PSO017G4760' => 'pso', 'PSO063G6716' => 'pso', 'PSO339G2873' => 'pso', 'PSO384G3560' => 'pso', 'PSO782G0945' => 'pso', 'PSO782G5343' => 'pso', 'QL02p071916' => 'qlo', 'QL03p054493' => 'qlo', 'QL07p022045' => 'qlo', 'RcHm_v2.0_Chr2g0174991' => 'rch', 'RcHm_v2.0_Chr2g0175091' => 'rch', 'RcHm_v2.0_Chr3g0480801' => 'rch', 'RcHm_v2.0_Chr4g0430881' => 'rch', 'Rhsim03G0011200' => 'rsi', 'Rhsim07G0057700' => 'rsi', 'Rhsim08G0044200' => 'rsi', 'Rhsim10G0008400' => 'rsi', 'Rhsim12G0029300' => 'rsi', 'RhsimUnG0058800' => 'rsi', 'Sabra06G0040100' => 'sbr', 'Sabra08G0135500' => 'sbr', 'Sabra10G0047700' => 'sbr', 'Sabra16G0055200' => 'sbr', 'Sabra16G0214400' => 'sbr', 'SalBow1G2543' => 'sbo', 'SalBow1G4337' => 'sbo', 'SalBow1G7980' => 'sbo', 'SalBow2G3094' => 'sbo', 'SalBow6G3510' => 'sbo', 'SalBow7G3408' => 'sbo', 'SalBow8G4921' => 'sbo', 'Sc03g0006660' => 'sci', 'Sc11g0000580' => 'sci', 'Sc13g0002030' => 'sci', 'Sed0006620' => 'sed', 'Sed0024623' => 'sed', 'SEGI_15233' => 'sgi', 'SEGI_26117' => 'sgi', 'SGA_v2.0_scaffold105G30460' => 'sas', 'SGA_v2.0_scaffold154G37163' => 'sas', 'SGA_v2.0_scaffold18G08214' => 'sas', 'SGA_v2.0_scaffold87G27138' => 'sas', 'SGA_v2.0_scaffold9G04767' => 'sas', 'SHI26351' => 'shi', 'SMO116G0140' => 'smo', 'Solyc02g092870.2' => 'sly', 'Solyc02g093980.3' => 'sly', 'Solyc03g005060.4' => 'sly', 'Solyc03g051790.3' => 'sly', 'Solyc05g015050.3' => 'sly', 'Sopen02g037440' => 'spe', 'Sopen02g038630' => 'spe', 'Sopen03g001070' => 'spe', 'Sopen03g011160' => 'spe', 'Sopen05g010280' => 'spe', 'Sp2g08030' => 'spa', 'Sp3g00250' => 'spa', 'Sp4g24490' => 'spa', 'Sp5g04910' => 'spa', 'Sp6g35940' => 'spa', 'TAR238G0001' => 'tar', 'TAR374G1191' => 'tar', 'TAR622G1247' => 'tar', 'TAR623G0621' => 'tar', 'TAR629G2365' => 'tar', 'TAR633G0230' => 'tar', 'THA.LOC104799318' => 'tha', 'THA.LOC104802359' => 'tha', 'THA.LOC104802377' => 'tha', 'THA.LOC104814192' => 'tha', 'Thecc.02G275900' => 'tca', 'Thecc.04G031000' => 'tca', 'Thecc.05G164900' => 'tca', 'Thhalv10003145m.g' => 'esa', 'Thhalv10005822m.g' => 'esa', 'Thhalv10012820m.g' => 'esa', 'Thhalv10016357m.g' => 'esa', 'Thhalv10020012m.g' => 'esa', 'Thhalv10022949m.g' => 'esa', 'TPR.G10083' => 'tpr', 'TPR.G3819' => 'tpr', 'TPR.G38342' => 'tpr', 'TPR.G7519' => 'tpr', 'TWI12G0671' => 'twi', 'TWI18G1414' => 'twi', 'TWI32G0280' => 'twi', 'unitig_0.g1944' => 'ugi', 'unitig_26.g10387' => 'ugi', 'unitig_26.g10388' => 'ugi', 'unitig_578.g15988' => 'ugi', 'unitig_748.g7056' => 'ugi', 'unitig_749.g13271' => 'ugi', 'vmacro01077' => 'vma', 'vmacro05941' => 'vma', 'vmacro07874' => 'vma', 'vmacro18332' => 'vma', 'VMungo0251G1484' => 'vmu', 'VMungo0251G2564' => 'vmu', 'VMungo0464G0221' => 'vmu', 'VMungo1383G2409' => 'vmu', 'VMungo1383G3317' => 'vmu', 'Zm00001eb005270' => 'zma', 'Zm00001eb034840' => 'zma', 'Zm00001eb093230' => 'zma', 'Zm00001eb182710' => 'zma', 'Zm00001eb182720' => 'zma', 'Zm00001eb316620' => 'zma', 'Zm00001eb415670' => 'zma' ) $gf_id = 'HOM05D001334' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001334' ) $data_identifier = 'HOM05D001334' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 6, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 18, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 6, 'mdo' => (int) 6, 'mtr' => (int) 2, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 8, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 7, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 2, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 3, 'ugi' => (int) 6, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb415670' $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